Abstract Laser Doppler velocity measurement technology has been widely used in the flow velocity measurement. To reduce the measurement error of Double Beam Laser Doppler Velocity Measurement System, in accordance of procedures and methods of measurement uncertainty provided by JJF1059—1999, the main sources of uncertainty in the flow velocity measurement were analysed from two aspects, one is the mathematical model, and the other is the measurement methods. A type and B type assessment were adopted, evaluation of uncertainty components in measuring results is obtained, and then combined standard uncertainty and extended uncertainty are got.